VIGGS:Variant information

Chr05:2697080 - 2703252

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2697094	A	G	47	1887.77	1.00	UTR_5_PRIME(\|182\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2697516	A	T	54	2357.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2697523	T	A	52	2322.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2697636	A	T	30	1321.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2697637	A	G	30	1321.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2698027	T	A	45	1790.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2698573	C	T	43	1579.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2698723	T	A	56	2297.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2698906	G	A	54	1991.77	1.00	SYNONYMOUS_CODING(SILENT\|agG/agA\|R138\|None\|Vigan.05G040400.01)	Vigna nepalensis
2699252	C	G	58	2336.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2699512	A	G	59	2377.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2699588	T	G	62	2443.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2699617	T	C	54	2197.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2699724	A	G	49	1937.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|4993\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2700055	G	C	56	2212.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|4662\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2700334	A	G	41	1718.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|4383\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2700641	G	A	62	2403.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|4076\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2700975	A	G	59	2361.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3742\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701269	G	A	53	2185.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3448\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701480	T	A	59	2644.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3237\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701517	A	C	53	2042.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3200\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701606	C	A	55	2226.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3111\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701617	G	A	61	2783.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3100\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701619	C	A	62	2783.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3098\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701690	G	T	62	2761.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3027\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701708	C	T	67	2707.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3009\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701818	A	T	64	2608.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2899\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701886	A	C	75	2992.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2831\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701925	C	T	64	2543.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2792\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701957	C	T	66	2900.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2760\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701980	A	C	65	2896.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2737\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701993	T	C	66	3049.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2724\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701996	T	C	69	3091.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2721\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702037	C	A	65	2654.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2680\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702085	G	A	56	2452.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2632\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702086	C	A	53	2452.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2631\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702168	T	G	43	1715.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2549\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702239	G	T	44	1715.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2478\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702273	A	G	39	1709.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2444\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702276	T	G	38	1580.77	0.97	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2441\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702282	A	G	41	1730.77	0.98	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2435\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702283	G	A	41	1730.77	0.98	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2434\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702341	G	A	34	1435.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2376\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702368	G	A	28	1198.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2349\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702371	A	G	28	1198.77	0.96	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2346\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702402	C	T	25	898.77	0.88	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2315\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702409	A	G	24	886.77	0.88	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2308\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702427	T	C	20	916.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2290\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702433	T	C	20	676.77	0.85	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2284\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702436	T	C	20	46.77	0.15	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2281\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702439	T	A	20	46.77	0.15	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2278\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702440	C	A	20	676.77	0.85	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2277\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702441	A	G	20	871.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2276\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702459	T	C	21	718.77	0.86	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2258\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702482	C	A	15	679.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2235\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702505	C	T	20	961.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2212\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702517	C	T	19	871.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2200\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702519	T	A	19	871.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2198\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702520	T	C	19	871.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2197\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702526	T	C	20	1006.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2191\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702536	A	G	25	1186.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2181\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702539	T	C	27	1231.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2178\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702544	T	C	28	1211.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2173\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702580	T	G	42	1598.77	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2137\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702721	A	C	59	2164.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|aAg/aCg\|K193T\|None\|Vigan.05G040400.01), UPSTREAM(\|1996\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702846	C	T	68	210.77	0.15	NON_SYNONYMOUS_CODING(MISSENSE\|Cca/Tca\|P235S\|None\|Vigan.05G040400.01), UPSTREAM(\|1871\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702848	A	G	70	240.77	0.14	SYNONYMOUS_CODING(SILENT\|ccA/ccG\|P235\|None\|Vigan.05G040400.01), UPSTREAM(\|1869\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702849	G	C	72	240.77	0.15	NON_SYNONYMOUS_CODING(MISSENSE\|Gac/Cac\|D236H\|None\|Vigan.05G040400.01), UPSTREAM(\|1868\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702870	G	A	78	450.77	0.21	NON_SYNONYMOUS_CODING(MISSENSE\|Gac/Aac\|D243N\|None\|Vigan.05G040400.01), UPSTREAM(\|1847\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702878	T	A	88	641.77	0.23	NON_SYNONYMOUS_CODING(MISSENSE\|caT/caA\|H245Q\|None\|Vigan.05G040400.01), UPSTREAM(\|1839\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702879	C	G	89	641.77	0.24	NON_SYNONYMOUS_CODING(MISSENSE\|Cta/Gta\|L246V\|None\|Vigan.05G040400.01), UPSTREAM(\|1838\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702952	G	C	86	1223.77	0.44	UPSTREAM(\|1765\|\|None\|Vigan.05G040500.01), UTR_3_PRIME(\|65\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2702978	A	G	100	1744.77	0.54	UPSTREAM(\|1739\|\|None\|Vigan.05G040500.01), UTR_3_PRIME(\|91\|\|None\|Vigan.05G040400.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2698176	TTG	T	38	1403.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2700239	AAT	A	53	2329.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|4477\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2700716	TTTTA	T	45	1910.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|4000\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701326	G	GTT	31	1455.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3390\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701340	T	TTG	45	2029.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3376\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701460	AAGGG	A	56	2567.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3256\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701580	GT	G	58	2305.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3136\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701674	GTTGTTTTT	G	60	2702.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|3042\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701973	C	CT	67	3215.74	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2743\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2701992	C	CCCACA	64	3016.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2724\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702485	TTCAAATTCTC	T	17	772.73	1.00	INTRON(\|\|\|None\|Vigan.05G040400.01), UPSTREAM(\|2231\|\|None\|Vigan.05G040500.01)	Vigna nepalensis
2702903	GTC	G	79	3453.73	1.00	UPSTREAM(\|1813\|\|None\|Vigan.05G040500.01), UTR_3_PRIME(\|17\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2702976	C	CCA	97	1879.73	0.48	UPSTREAM(\|1740\|\|None\|Vigan.05G040500.01), UTR_3_PRIME(\|90\|\|None\|Vigan.05G040400.01)	Vigna nepalensis
2702977	T	TAG	97	1879.73	0.46	UPSTREAM(\|1739\|\|None\|Vigan.05G040500.01), UTR_3_PRIME(\|91\|\|None\|Vigan.05G040400.01)	Vigna nepalensis